High-level changes

Improved compatibility with different FCS files.
Improved ability to handle high-resolution FCS data and floating-point data, and transform this data to MEF.
Logicle scale implemented. This is the new default for plotting.

Important code changes

gate.density2d and all simple plotting functions now include arguments xscale, yscale, and zscale as appropriate, to define the scale of each axis. Valid options are 'linear', 'log', and 'logicle'. All these functions default to logicle.
Arguments log, xlog, ylog, and zlog in plotting functions are deprecated.

FCSData property domain has been deprecated. New function range returns, for each specified channel, the lower and upper bounds as specified by the FCS file.
FCSData property hist_bin_edges has been deprecated. New function hist_bins allows for dynamic generation of histogram bins using either linear, logarithmic, or logicle scaling.

The transformation function returned by get_transform_fxn is now meant to be used with data previously transformed to RFI using transform.to_rfi().
Functions clustering_gmm and selection_std now allow for rescaling of the data before performing their operations. The default scaling is logicle.
fit_beads_autofluorescence now uses a model that transforms data from RFI to MEF. Previously, the model was meant to be used to transform data in raw channel numbers to MEF, when using a logarithmic amplifier. The new approach allows for transformation of data taken with linear amplifiers as well.